Most of the time, the plot is about the heroes risking corruption; occasionally, though, the hero is playing a Batman Gambit of their own, banking on either crippling the evil organization or genuinely making it a force for good.

In Superman & Batman: Generations, Bruce Wayne accepts Ra's al-Ghul's offer of succeeding him as the head of the League of Shadows, then changes it from a legion of assassins into a benevolent superpower. This turned out to be fairly simple; it was just a process of taking the cover organizations they used to aid in their evil plans and making them legit.

In Superman: World of New Krypton, General Zod is severely injured before he can unleash his plan to invade Earth. While he recovers, the supreme commander of New Krypton's military forces is ... Commander Kal-El. Kryptonian foreign policy suddenly becomes a lot more diplomatic; unfortunately, it's temporary.

In the Marvel Universe, the Shroud set up a gang called the Night Shift. The other members thought they were preying on the organised crime gangs of LA so they could take over the city. Actually, he was just using them to shut down organised crime in LA.

In The Sandman, after Lucifer quits, throws everyone out of Hell, and hands the keys over to Morpheus, God decides that Hell will be run directly by Heaven from now on and appoints two angels to be his overseers there.

Later it's revealed that only one of these angels was properly good. The other was indecisive, having stayed impartial from the original War in Heaven and picking the winning side as soon as it came apparent. He develops some serious Smug Snake and Holier Than Thou tendencies soon enough after taking charge of Hell.

The good angel was also the one who had the courage to take the key to Hell. The other one whimpered, wailed, and even considered following Lucifer's example by rebelling against God before resigning himself to his duty.

In the League of Extraordinary Gentlemen, it was revealed that Moriarty was a member of British Intelligence who took over Britain's organized crime networks as part of a plan to keep crime in the country within limits. Unfortunately, he ended up Becoming the Mask, at which point he was stopped first by Sherlock Holmes, and then by the League.

"Good" is a stretch in this case, but at one point The Punisher took over a mafia family so use their resources to take even worse criminals out.

In Ghost Rider, Noble Kale takes over Mephisto's realm, which effectively put an end to Mephisto and Blackheart for good, or would have if StatusQuo wasn't so prevalent in Marvel comics. So he was kicked out of hell by demons for being too benevolent for their tastes and later disappeared into comic book limbo while Mephisto and Blackheart returned.

A Song of Ice and Fire features a variation where Daenerys conquers a slave city using an army of slaves she bought and then freed, and then decides to settle down and rule rather than leave its people to starve. She then has to deal with the city itself, whose entire economy depended on slavery. Like most of Martin's works, institutional problems prove hard to fix from the top down.

In Atlas Shrugged, the looters eventually capture John Galt because they want him to be their new leader. He refuses.

Live Action TV

Angel. In Season 5, Team Angel are put in charge of the Los Angeles branch of supernatural law firm Wolfram & Hart. It doesn't work well, with our heroes finding themselves increasingly morally compromised and demoralized. Wolfram & Hart were fairly open about this being the point of giving them the job.

The Prisoner (1967) episode "Free For All": Number 6 is elected to the position of Number 2, technically putting him in charge of the Village.

In Chuck, Mary Bartowski is right-hand man of Alexei Volkoff, head of Volkoff Industries.

In Torchwood, Captain Jack was pressured into working for Torchwood Three back when it was still a conspiracy to seize alien tech for the British Empire and hunt down the Doctor. He was given the opportunity to reinvent the organization when its previous leader went mad after seeing the future and killed everyone.

In Arrow, Ollie nearly ends up running the League of Assassins after the current Ra's al Ghul makes him his heir (in their duel, he'd handed Ollie a total Curb-Stomp Battle but considered Oliver's survival proof of his worth.) Oliver is told that when he's officially in charge, his desires will be law, even if it's to become a lawkeeping force under the Arrow. What keeps him from taking over and trying to turn the League into Heroes "R" Us? Mainly, their tradition to destroy the hometown of a new leader in order to sever all past ties. Uh-oh.

In Supergirl the Department of Extranormal Operations was founded specifically to act as a counter to Superman if necessary, which evolved into a Knight Templar organization that considered all extraterrestrials as threats, run by rabid bigot Hank Henshaw who saw its responsibility as protecting humans from aliens at almost any cost. When J'onn J'onzz secretly replaced Henshaw, he was obviously able to quietly adjust its mission and personnel to the point that when Supergirl became active the DEO aided her, and when he was outed as a Martian the majority of people within the organization took it in stride and cheered when he was formally re-instated as director under his true name. The DEO has since become one of the biggest protectors of law-abiding and innocent extraterrestrials in the United States.

Mythology & Religion

There is one train of philosophical thought that proposes this is how Heaven and Hell work. If God is all powerful, and if He created everything, and if He has a plan for everything, then logically Hell operates because God wants it to operate. And since God's plan predetermines everything that happens in the universe, this includes everything that happens in Hell, too. Thus, God is actually running Hellnote Technically Hell does not exist yet: people are to be sorted into Heaven or Hell on Judgement's Day and no earlier. But he will be running Hell. As well as every single evil organization, evil person, or evil action, ever. This oddity is known as "the problem of evil." Traditional Calvinism took it to the extreme of saying God had predestined everyone's fate, including what actions they would take to save or damn them, and that one could guess who "the elect" (i.e. those going to heaven) would be by their upright, successful lives, versus the damned having the exact opposite.

Tabletop Games

In Magic: The Gathering's Ravnica cycle, Jarad takes over as Guildmaster of the Golgari after Savra is defeated.

The Mass Effect 2 DLC "Lair of the Shadow Broker" ends with Commander Shepard and Liara T'soni killing the Shadow Broker and Liara deciding to take over his organization and use it to help Shepard fight the Reapers.

In the end of Mass Effect 3, one of the three options to stop the Reaper threat is to upload Shepard's consciousness to control them. The consequences of this are never shown though in the original ending, with the exception of the Reapers leaving. In the Extended Cut version of this ending, the resulting Reaper-Shepard consciousness has the Reapers repair all the damage they caused and vows to honor the sacrifice the human Shepard made by defending the galaxy.

At the end of Outlast, Miles ends up becoming the new host for the Walrider, and is last seen during the Whistleblower DLC using his newfound powers to take vengeance on all the bastards at Murkoff who put him and the other inmates through a living hell.

Sub-Zero went from being a renegade on the run from the Lin Kuei, a shady assassin clan from China, to becoming the clan's leader and changing its purpose to protecting Earthrealm from outside threats.

At the end of Wrath of the Lich King, the titular Lich King is defeated. But somebody has to be in charge of the hordes of ravenous undead crawling around the planet, or the effects will be worse than the original war. So Bolvar Fordragon takes on the mantle of the Lich King, proclaiming himself the "Jailor of the Damned."

Throughout the series, you can choose to play as a good character, an evil character, or any shade of gray in between. If you choose to play as a "good" character, you can still rise to the top of multiple "evil" organizations, such as the Dark Brotherhood (an assassin's guild doubling as a Religion of Evil) and the Thieves' Guild (which has rules like no-killing but is still a group centered around stealing the property of others). This also works in reverse, as you can be an outright evil character who murders unprovoked and steals everything that isn't nailed down, yet rise to the top of several "good" factions like honorable warrior guilds and temple organizations, as long as you don't kill or steal from your fellow members.

In Oblivion's Knights of the Nine expansion, a certain quest wipes away your infamy and is supposed to offer redemption for evil characters. You can be the most thoroughly cruel Dark Brotherhood assassin and head of the Thieves' Guild, but complete the quest and be seen as a virtuous, noble paragon.

Prince Zuko of Avatar: The Last Airbender technically ends up in this role in the finale. While the Fire Nation is an evil, corrupt, warmongering empire, it's explicitly pointed out that this is because propaganda has raised everyone to believe its necessary, even good. They aren't Always Chaotic Evil. Zuko himself spent about two and a half seasons realizing it was wrong, and eventually pulled a Heel–Face Turn. When the finale comes around and Team Avatar places him in charge, he's more than happy to rebuild the nation. Follow-up comics make it clear how very, very hard this is, especially when everyone has been conditioned to hate you and you're simultaneously trying to fix an entire nation while not being as authoritarian as your father (though canonically he survives, abdicates his position to his daughter, and is still traveling as an ambassador at ninety-three, as per the sequel show).

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